Hi Elaine, <br><br>&nbsp;Thanks a lot for such a detailed reply.&nbsp; I higly appreciate your time. I have a last question, I hope you won&#39;t mind it. In chimera website there is a option for user specified partial charges... I spend a lot of time to use a Define attribute: but no success so far. How can I change the partial charge of FE in heme using define attribute. 
<br><br>Once again, thank you very much for your time and help.<br>best regards<br>s<br><br><a name="user-specified">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html<br></a>